Milky Ways

25 Apr

Milk received during the first year or two of an infants life has a great effect on its development. Human milk consists of key proteins that have a wide range of functions, including but not limited to : carrying of minerals or insoluble vitamins and other compounds,  being stabilizers, breaking down lipids and containing components of both innate and acquired immune defense systems. Together with other components of milk, proteins may also contribute to the selection and establishment of an appropriate microbiome in the gut of the infant. [1]

Benefits of breastfeeding mammalian milk vs non-breastfeeding formula [1] South Carolina Department of Health and Environmental Control

The understanding of the human milk proteome and how it changes with time during lactation and in disease is developing rapidly, and could play a key role to further understanding development in children . There is considerable interest now in the microbiome of infants and how it relates to present and future health. Milk which serves as vehicle for the delivery of appropriate microbes to the newborn’s gut, and may hold the key to controlling and refining the nature of the microbiome. [3]

lecture on the human milk microbiome

A full understanding of human milk and how it changes in health and disease may either lead to improvements in the design of artificial formula, or an increased realization that such formulations cannot fully substitute for all of the functions of milk produced by the females of a species for its own young as described above in the cart. [2]


3- DC gel electrophoresis of the human milk protein showing 26 distinct protein bands. [1]

The further understanding of the composition of human gut is essential for a variety of reasons .In this study, human milk was analyzed for the presence of proteins and bacteria. Very little work had been previously done to characterize the full diversity of the milk bacterial communities along with their stability  over time. Using pyrosequencing of the 16s ribosomal RNA gene, the bacterial communities were accurately characterized. Milk samples were taken from 16 women, three times over a four week period and analyzed. The results indicated that milk bacterial communities were generally very complex and stable over the period of four weeks. In fact there were several genera of bacteria found in the milk that were previously thought not to exist in milk ! The study demonstrated the long standing notion that human milk benefits the infant far greater than any formula. The results showed that human milk contains a collection of bacteria that was far more diverse that previously imagined. This of course could lead to changes in formula by adding more bacteria and proteins found in human milk.


the proteins of bovine milk and a bovine-based whey-dominant infant formula were compared with those of human milk for infants . The protein distribution of infant formula differed significantly from that of either type of human milk [4]. Researchers performed a two and a half year study assembling the human infant gut microbiome. They related life events in development of infants to furthered microbiome composition. Infants who used bovine milk and a bovine-based whey-dominant infant formula were compared with those of human milk for infants  By collecting fecal samples from healthy infants, analysis of over 300,00 16s RNA genes indicated that diversity of the microbiome increase gradually over time . Infants given human breast milk were healthier and grew faster in this small sample (just six infants). More research is needed to validate this study.

[1]. P Roncada, Stipetic L, et al. Proteomics as a tool to explore human milk in health and disease. Journal of Proteomics.

[2] E. Forsum, B. Lonnerda. Variation in the contents of nutrients of breast-milk during one feedinNutr Rep Int, 19 (1979), pp. 815–820

[3] Koenig JE, Spor A et al, Succession of microbial consortia in the developing infant gut microbiome. Department of Microbiology, Cornell University.

[4] Wynn PC, Morgan A, Sheehy P, Milk Proteins/Minor proteins, Bovine Serum Albumnn. Encylopedia of Dairy Sciences . Academic Press San Diego 2011 (

[5] Hunt KM, Foster JA, Forney LJ, Schütte UME, Beck DL, et al. (2011) Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk. PLoS ONE 6(6): e21313. doi:10.1371/journal.pone.0021313


Clonorchis sinensis: Should we be afraid?

18 Apr

Clonorchis sinensis is a Chinese liver fluke that effects the human liver . Clonorchis sinensis is a parasite found within the liver but has been found in the gall bladder and bile duct . An estimated 30,000,000 humans are effected by it with the highest concentrations of those effected being in southeastern Asian countries  of Japan , China and Korea [1] . The egg of the clonorchis sinensis is first consumed in fresh water by a snail as it floats throughout the water . The snail serves as the first intermediate host for the parasite . The most common snail host is the Parafossarulus manchouricus . The snail consumes the miracidium which hatches from the egg consumed by the snail and grows inside of it parasitically . The next stage of development is the sporocyst stage in which the miracidium turns into the sporocyst. The sporocyst houses the asexual reproduction of redia. The redia house cercaria . Cercaria are free swimming and develop in large numbers quickly also through asexual reproduction . [2]

[6] Sao Francisco

[6] Sao Francisco

Once the redia have matured they leave the snail and move on to their second intermediate host . The parasite seeks out fish as a host , boring their way into fish muscle . Once inside the parasite interestingly creates a protective metacercarial cysts. This cysts surrounds the body providing body Armour as protection . The cyst allows for the successful transfer to its final host : the human liver as the fish is consumed . Essentially the cyst the parasite from being digested by gastric acids allowing the Clonorchis sinensis to travel unharmed throughout our digestive tract .
Center for Disease Control

Center for Disease Control [5]

Clonorchis sinensis feed on human bile in the liver and reproduce eggs nearly every 30 seconds or less. So what effect does this parasite have on us ? Clonorchis causes inflammatory reactions in the bile . [3] Commonly causes epithelial hyperplasia and cholangiocarcinoma . It is possible that the parasite could consume all of the bile in your liver which in turn stops the body from digesting anything !

In general Clonorchis sinensis is asymptomatic but in acute phases abdominal pain nausea and diarrhea can occur . In longer persistent cases fatigue ,anorexia and extreme weight lost are common amongst others . Treatment of Clonorchis sinensis is through a cycle of drugs . [4]

1. Clonorchis FAQs. 2012. Global Health- Divison of Parasitic Disease and Malaria. CDC – Center for Disease Control

2. Erckload E, Lee H. Clonorchis sinesis. ADW: Animal Diversity  Web.

3. Brusca, R., G. Brusca. 1990. Invertebrates. Sunderland, Massachusetts: Sunauer Associates, Inc.

4. Park DH, Son HY. Clonorchis sinensis, images in clinical medicine. N Engl J Med 2008; 358:16.



Microchimerism fetus to parent

11 Apr

Microchimerism, is a fascinating part of biology in that is relates to all of us through human reproduction. It is characterized by the presence of  a small number of cells that originate from another individual and are genetically distinct from the host cells. [1]  Surprisingly, some mother’s cells can be found in her adult offspring and some cells from the fetus can be found in the mother decades later.  [2]. But just what effect do these foreign cells have on the host? Studies have shown that they can be both beneficial and harmful. The list of potential diseases include but are not limited to autoimmune diseases like rheumatoid arthritis and type 1 diabetes, degenerative diseases and cancer.  Autoimmune diseases are of course characterized by cells in your own body attacking one another. [3] Fetal michrochimerism recently was linked to several of these autoimmune diseases stemming from terminated pregnancies. With an increase in the number of autoimmune diseases in the past four decades there is reason to believe that this increase may be related directly to the utilization of abortion. [4] More research on this entire topic is needed.


Fetal microchimerism is a relatively recent discovery in that  publications only date back to the late 1970s . During fetal microchimerism intact living cells from the fetus and maternal parent circulate back and forth to one another. This occurs in all pregnancies and increases as the development of the fetus occurs. Meaning that it is a bidirectional process where: maternal microchimerism is maternal cells transferred to the fetus and fetal microchimerism is fetal cells to the maternal parent. Male fetal cells have been demonstrated in both maternal synovial tissue and skin of patients with rheumatoid arthritis and in the skin and blood of women with systemic sclerosis. Furthermore these fetal cells were detected in maternal tissue as long as 27 years after birth! [5]

How exactly do these cells become active? The role activating the hibernating fetal microchimeric cells are speculated to be activated by viral, bacterial agents, drugs or abnormal local tissue proteins, but the exact reason is unknown.

Is any group at higher risk than another? Women who had an elective abortion in either the first or second trimester have an greater risk for fetal microchimerism and the risk of developing an auto-immune disease for the rest of their lives. This topic is extremely interesting and further research is needed as information has reached just the “tip of the iceburg.”

Figure 1


Our Environment is Quite Complex

4 Apr

Metagenomics also referred to as “community genomics” or “environmental genomics”, is the sequencing and analysis of DNA of microorganisms recovered from an environment, without the need for culturing them. [1] Currently we have very little information on the vast majority of microorganisms present on earth. Estimates are that less than 1 % of all bacterial species have been cultured! In fact most of our knowledge about ancient evolutionary organisms is from data associated with organisms that have common links and have been studied vigorously like plants and cultured microbes. With metagenomic studies on the rise there is a potential to unlock new areas of gene evolution.

[2] National Academy of Science

In a recent study done on the Global Ocean Sampling expedition data potentially break through discoveries were made. Researchers at the University of California designed and implemented new methods for analyzing metagenomic data and applied them to the GOS data. These new methods created in a computer program called STAP detected ss-RNA genes that branch very deeply in the tree of life. ” This automated system: (1) identifies ss-rRNA coding sequences in the metagenomic data set; (2) generates an alignment of each of those ss-rRNA gene sequences against a prealigned set of representative ss-rRNA sequences from the three domains of life; (3) builds phylogenetic trees from each of these alignments; and (4) identifies those trees in which the environmental sequence branches very deeply, i.e., either between the three domains or as one of the deepest branches within a domain (assuming that each domain is a monophyletic group” [3] In the study they explored data to answer the question Can we identify novel rRNAS or protein coding that suggest the existence of additional major branches on the tree of life?

They searched for lineages in three gene families: small subunit rRNA, recA and rpoB superfamilies. Although more studies on this topic are needed it was discovered that there are multiple branches in the recA and rpoB gene families. They suggested three possibilites for the links in metagenomic data. But the data yielded to the notion that the novel sequences are consistent with the possibility that they come from a new (i.e., fourth) major branch of cellular organisms on the tree of life. Further studies are needed in order to determine the source of these sequences and then targeted metagenomics will help determine whether the novelty extends to all genes in the genome. [3]


[1] Seshardi, R. What is Metagenomics? CAMERA:  Marine Microbiology Ecology.


[3]Wu D, Wu M, Halpern A, Rusch DB. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PloS ONE. 2011;6:e18011.

Lichens can do what!?

2 Apr

Transmissible spongiform encephalopathies (TSEs) are a group of infectious , neurogenerative disease. TSE’s however, are unlike most pathogens in that they demonstrate high levels of stability and resist most conventional forms of decontamination. This of course can lead to many problems when attempting to control and deter the effects of this neurogenerative disease. Some diseases that TSE are present in, and occur relatively frequently are CJD which is caused by surgical instrument contamination, scarpie and CWD which readily enters the environment through infected sheep and animals through shedding, salvia , urine and dead carcasses.  The realization that these factors can remain infectious in the environment has lead to research on degradation and control of transmission of TSEs.

Brief Video describing CJD by the Mayo Clinic [1]


Where exactly do lichens come in? Lichens which are a symbiotic relationship between fungi and a photosynthetic partner with either green algae or sometimes cyanobacterium. Lichens are an omnipresent  group meaning they are found in almost all environments including artic conditions due to their ability to fix carbon. In order to survive lichens produce unusual organic compounds that aid their survival. These compounds have potential antibiotic, antiviral and other chemotherapeutic applications.  In this study the uniqueness and diversity of lichens was used to test their capabilities of  inactivating or degrading the TSES in the form of rogue proteins known as prions. The study which was done in vitro, was done with the hope that the lichens would enable organisms to produce molecules capable of inactivating or degrading prions. IT was found that extracts of three lichen species have a serine protease activity capable of of reducing TSEs in vitro. More studies on this topic need to be done however, with positive results their is the possibility that lichens can be used as part of treatment against TSEs.


[2] Johnson, Christopher J., and James P. Bennett. “Degradation of the Disease Associated Prion Protein by a Serine Protease from Lichens.” Plos One. Open Access, n.d. Web. 1 Apr. 2013.